AUTHOR=Du Zhaokui , You Shixian , Yang Dang , Tao Yutian , Zhu Yunxiao , Sun Wen , Chen Zhengman , Li Junmin 

TITLE=Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1048822

DOI=10.3389/fpls.2022.1048822

ISSN=1664-462X

ABSTRACT=<sec><title>Background</title><p><italic>Kandelia obovata</italic> is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (<underline>N</underline>AM, <underline>A</underline>TAF1/2 and <underline>C</underline>UC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of <italic>K. obovata NAC</italic> genes (<italic>KoNACs</italic>) and their responses to chilling stress have rarely been studied.</p></sec><sec><title>Methods</title><p>The <italic>KoNAC</italic> gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the <italic>KoNACs</italic> that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.</p></sec><sec><title>Results</title><p>A total of 79 <italic>KoNACs</italic> were identified, and they were unequally distributed across all 18 chromosomes of <italic>K. obovata</italic>. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of <italic>Arabidopsis thaliana</italic>. The <italic>KoNACs</italic> exhibited greater synteny with <italic>A. thaliana</italic> sequences than with <italic>Oryza sativa</italic> sequences, indicating that <italic>KoNACs</italic> underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of <italic>KoNAC</italic> genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some <italic>KoNAC</italic> genes showed tissue-specific expression, suggesting that these <italic>KoNACs</italic> might be important for plant development and growth. Additionally, the expression levels of 19 <italic>KoNACs</italic> were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these <italic>KoNACs</italic> might play important roles during cold stress responses and might be candidate genes for the genetic engineering of <italic>K. obovata</italic> with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 <italic>KoNACs</italic> and 284 other genes) were significantly correlated.</p></sec><sec><title>Conclusions</title><p>Seventy-nine <italic>KoNACs</italic> were identified in <italic>K. obovata</italic>, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of <italic>KoNACs</italic> engaged in chilling stress. Our results lay the foundation for evolutionary analyses of <italic>KoNACs</italic> and their molecular mechanisms in response to environmental stress.</p></sec>